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The uneven rainfall distribution, limited soil nutrients, and continuous cropping effect in the Loess Plateau restrict the sustainable development of fruit tree/crop (soybean and maize) intercropping systems. A two-year field experiment was conducted to investigate the effects of different water and fertilizer regimes on the soil nutrients and growth of intercropping systems during the crop replacement period. The experiment involved three irrigation levels (0% (I₀), 50% (I₁), and 80% (I₂) of field capacity), two irrigation methods (drip irrigation (DI) and flood irrigation (FI)), and three fertilizer application rates (0 (F₀), 375 (F₁), and 750 (F₂) kg/hm²). The results showed that in 2020 and 2021, the soil water contents increased with increasing irrigation and fertilization. The soil ammonium nitrogen, nitrate nitrogen, and soil organic matter contents in 2021 were 21.0%–68.4% higher than those in 2020. Increasing the fertilizer application rate improved the photosynthesis rate and transpiration rate of apples and maize in 2020 but had a reverse U-shape effect on soybeans in 2021. Irrigation and fertilization increased soybean and maize yields by 2.9%–30.5% compared with the I₀F₀ treatment. The maize root indicators generally showed an increasing trend followed by a decreasing trend with increasing fertilizer application in 2020, while soybean exhibited an opposite pattern in 2021. The FI₁F₁ and DI₂F₂ treatments yielded the optimal economic benefit in 2020 and 2021, respectively. Therefore, from an economic standpoint, FI and DI would have been recommended in 2020 and 2021, respectively. Factor analysis suggested that the DI₂F₂ treatments had the highest comprehensive benefits over the two years studied. Therefore, we recommend using DI combined with 80% field capacity irrigation and 750 kg/hm² fertilization to maximize the comprehensive benefits of intercropping systems during the crop replacement period.